Hi Bruce, i tried your suggestion but it is saying Missing file name. Do i need to include wm.mgz in the command line?
Regards, Michael bash-4.1$ freesurfer_setup_freeview -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer_v6.0.0 FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects MNI_DIR /usr/local/freesurfer_v6.0.0/mni FSL_DIR /usr/local/fsl bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj2/Subj2 bash-4.1$ recon-all -autorecon2-wm -autorecon3 -s Subj2 if: Missing file name. bash-4.1$ ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: 20 June 2017 19:10:10 To: Freesurfer support list Subject: Re: [Freesurfer] Regenerating the WM Volume surface can you include your full command line? It looks like you typed: recon-all -autorecon2-wm -autorecon3 -Subj2 when probably what you wanted was recon-all -autorecon2-wm -autorecon3 -s Subj2 cheers Bruce On Tue, 20 Jun 2017, Michael Davies wrote: > > Hello, i am currently having problems with the code required to regenerate > the surface when editing the WM Volume. I was wondering if you could provide > any tips or advice as > to where i am going wrong please? > > Kind regards, Michael > > bash-4.1$ freesurfer_setup_freeview > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > FSL_DIR /usr/local/fsl > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj2/Subj2 > bash-4.1$ recon-all -autorecon2-wm -autorecon3 -Subj2 > ERROR: Flag -Subj2 unrecognized. > -autorecon2-wm -autorecon3 -Subj2 > Linux pbic.bham.ac.uk 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 > UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s exited with ERRORS at Tue Jun 20 19:58:38 BST 2017 > > For more details, see the log file > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > >
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